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. 2016 Sep 28;80(4):955–987. doi: 10.1128/MMBR.00029-16

TABLE 2.

The complete gene set of MiniBacilluse

Gene BSU no.a Essentialb Syn3.0c EC no. PDB accession no. Organismd Function(s)
Information
    DNA replication
        dnaA BSU00010 Yes Yes 2Z4R Thermotoga maritima Replication initiation protein
        dnaB BSU28990 Yes Initiation of chromosome replication
        dnaC BSU40440 Yes Yes 3.6.4.12 2VYE Geobacillus kaustophilus Replicative DNA helicase
        dnaD BSU22350 Yes 2V79 B. subtilis Initiation of chromosome replication
        dnaE BSU29230 Yes Yes 2.7.7.7 3E0D Thermus aquaticus DNA polymerase III (alpha subunit)
        dnaG BSU25210 Yes Yes 2.7.7.- 4E2K S. aureus DNA primase
        dnaI BSU28980 Yes Yes 4M4W B. subtilis Primosome component (helicase loader)
        dnaN BSU00020 Yes Yes 2.7.7.7 4TR6 B. subtilis DNA polymerase III (beta subunit), beta clamp
        dnaX BSU00190 Yes Yes 2.7.7.7 1JR3 E. coli DNA polymerase III (gamma and tau subunits)
        holA BSU25560 Yes Yes 2.7.7.7 3ZH9 B. subtilis DNA polymerase III, delta subunit
        holB BSU00310 Yes 2.7.7.7 1NJG E. coli DNA polymerase III (delta subunit)
        ligA BSU06620 Yes Yes 6.5.1.2 2OWO E. coli DNA ligase (NAD dependent)
        priA BSU15710 Yes 3.6.4.- 4NL4 Klebsiella pneumoniae Primosomal replication factor Y
        polC BSU16580 Yes Yes 2.7.7.7 3F2B G. kaustophilus DNA polymerase III (alpha subunit)
        rtp BSU18490 No 1BM9 B. subtilis Replication terminator protein
        ssbA BSU40900 Yes Yes 3VDY B. subtilis Single-strand DNA-binding protein
        yabA BSU00330 No 5DOL B. subtilis Inhibitor of DnaA oligomerization
        polA BSU29090 No Yes 2.7.7.7 1BGX T. aquaticus DNA polymerase I
    Chromosome maintenance
        scpA BSU23220 Yes 3ZGX B. subtilis DNA segregation/condensation protein
        scpB BSU23210 Yes Yes 3W6J Geobacillus stearothermophilus DNA segregation/condensation protein
        smc BSU15940 Yes Yes 3ZGX B. subtilis SMC protein
        parE BSU18090 Yes Yes 5.99.1.- 4I3H Streptococcus pneumoniae Subunit of DNA topoisomerase IV
        parC BSU18100 Yes Yes 5.99.1.- 2INR S. aureus Subunit of DNA topoisomerase IV
        spoIIIE BSU16800 No 2IUT Pseudomonas aeruginosa ATP-dependent DNA translocase
        sftA BSU29805 No 2IUT P. aeruginosa DNA translocase
        codV BSU16140 No 1A0P E. coli Site-specific integrase/recombinase
        ripX BSU23510 No 1A0P E. coli Site-specific integrase/recombinase
        gyrB BSU00060 Yes Yes 5.99.1.3 4I3H S. pneumoniae DNA gyrase (subunit B)
        gyrA BSU00070 Yes Yes 5.99.1.3 4DDQ B. subtilis DNA gyrase (subunit A)
        topA BSU16120 Yes Yes 5.99.1.2 4RUL E. coli DNA topoisomerase I
        hbs BSU22790 Yes 1HUE G. stearothermophilus Nonspecific DNA-binding protein HBsu
    Transcription
        rpoA BSU01430 Yes Yes 2.7.7.6 3IYD E. coli RNA polymerase alpha subunit
        rpoB BSU01070 Yes Yes 2.7.7.6 3IYD E. coli RNA polymerase beta subunit
        rpoC BSU01080 Yes Yes 2.7.7.6 3IYD E. coli RNA polymerase beta′ subunit
        sigA BSU25200 Yes Yes 3IYD E. coli RNA polymerase sigma factor SigA
        rpoE BSU37160 No 2.7.7.6 2KRC B. subtilis RNA polymerase delta subunit
        helD BSU33450 No 3.6.4.12 DNA 3′–5′ helicase IV
        greA BSU27320 No Yes 1GRJ E. coli Transcription elongation factor
        nusA BSU16600 Yes Yes 1HH2 T. maritima Transcription termination factor
    RNA folding and degradation
        cspD BSU21930 No 1C9O Bacillus caldolyticus Cold shock protein
        cspB BSU09100 No 2ES2 B. subtilis Major cold shock protein
        rny BSU16960 No Yes 3.1.4.16 RNase Y
        rnjA BSU14530 Yes Yes 3ZQ4 B. subtilis RNase J1
        pnpA BSU16690 No 2.7.7.8 3CDI E. coli Polynucleotide phosphorylase
        nrnA BSU29250 No Yes 3.1.3.7 3DEV Staphylococcus haemolyticus Oligoribonuclease (nano-RNase)
    Aminoacyl tRNA synthetases
        alaS BSU27410 Yes Yes 6.1.1.7 3HTZ E. coli Alanine-tRNA synthetase
        argS BSU37330 Yes Yes 6.1.1.19 3FNR Campylobacter jejuni Arginyl-tRNA synthetase, universally conserved protein
        asnS BSU22360 Yes Yes 6.1.1.22 1X54 Pyrococcus horikoshii Asparagyl-tRNA synthetase
        aspS BSU27550 Yes Yes 6.1.1.12 1EQR E. coli Aspartyl-tRNA synthetase
        cysS BSU00940 Yes Yes 6.1.1.16 3TQO Coxiella burnetii Cysteine-tRNA synthetase
        gatC BSU06670 Yes 6.3.5.7 2DF4 S. aureus Production of glutamyl-tRNAGln
        gatA BSU06680 Yes Yes 6.3.5.7 2DF4 S. aureus Production of glutamyl-tRNAGln
        gatB BSU06690 Yes Yes 6.3.5.7 2DF4 S. aureus Production of glutamyl-tRNAGln
        gltX BSU00920 Yes Yes 6.1.1.17 2O5R T. maritima Glutamyl-tRNA synthetase, universally conserved protein
        glyS BSU25260 Yes 6.1.1.14 Glycyl-tRNA synthetase (beta subunit)
        glyQ BSU25270 Yes 6.1.1.14 1J5W T. maritima Glycyl-tRNA synthetase (alpha subunit)
        hisS BSU27560 Yes Yes 6.1.1.21 1QE0 S. aureus Histidyl-tRNA synthetase
        ileS BSU15430 Yes Yes 6.1.1.5 1QU2 S. aureus Isoleucyl-tRNA synthetase
        leuS BSU30320 Yes Yes 6.1.1.4 1OBH Thermus thermophilus Leucyl-tRNA synthetase
        lysS BSU00820 Yes Yes 6.1.1.6 3E9H G. stearothermophilus Lysyl-tRNA synthetase
        metS BSU00380 Yes Yes 6.1.1.10 4QRD S. aureus Methionyl-tRNA synthetase
        pheT BSU28630 Yes Yes 6.1.1.20 2RHS S. haemolyticus Phenylalanyl-tRNA synthetase (beta subunit)
        pheS BSU28640 Yes Yes 6.1.1.20 2RHQ S. haemolyticus Phenylalanyl-tRNA synthetase (alpha subunit), universally conserved protein
        proS BSU16570 Yes 6.1.1.15 2J3L Enterococcus faecalis Prolyl-tRNA synthetase
        serS BSU00130 Yes Yes 6.1.1.11 2DQ3 Aquifex aeolicus Seryl-tRNA synthetase
        thrS BSU28950 No Yes 6.1.1.3 1NYQ S. aureus Threonyl-tRNA synthetase (major)
        trpS BSU11420 Yes Yes 6.1.1.2 3PRH B. subtilis Tryptophanyl-tRNA synthetase
        tyrS BSU29670 Yes Yes 6.1.1.1 2TS1 G. stearothermophilus Tyrosyl-tRNA synthetase (major)
        valS BSU28090 Yes Yes 6.1.1.9 1GAX T. thermophilus Valyl-tRNA synthetase
    Ribosomal proteins
        rplA BSU01030 No Yes 3J9W B. subtilis Ribosomal protein L1
        rplB BSU01190 Yes Yes 3J9W B. subtilis Ribosomal protein L2
        rplC BSU01160 Yes Yes 3J9W B. subtilis Ribosomal protein L3
        rplD BSU01170 Yes Yes 3J9W B. subtilis Ribosomal protein L4
        rplE BSU01280 Yes Yes 3J9W B. subtilis Ribosomal protein L5
        rplF BSU01310 Yes Yes 3J9W B. subtilis Ribosomal protein L6
        rplI BSU40500 No Yes 3J9W B. subtilis Ribosomal protein L9
        rplJ BSU01040 Yes Yes 3J9W B. subtilis Ribosomal protein L10
        rplK BSU01020 No Yes 3J9W B. subtilis Ribosomal protein L11
        rplL BSU01050 Yes Yes 3J9W B. subtilis Ribosomal protein L12
        rplM BSU01490 Yes Yes 3J9W B. subtilis Ribosomal protein L13
        rplN BSU01260 Yes Yes 3J9W B. subtilis Ribosomal protein L14
        rplO BSU01350 No Yes 3J9W B. subtilis Ribosomal protein L15
        rplP BSU01230 Yes Yes 3J9W B. subtilis Ribosomal protein L16
        rplQ BSU01440 Yes Yes 3J9W B. subtilis Ribosomal protein L17
        rplR BSU01320 Yes Yes 3J9W B. subtilis Ribosomal protein L18
        rplS BSU16040 Yes Yes 3J9W B. subtilis Ribosomal protein L19
        rplT BSU28850 Yes Yes 3J9W B. subtilis Ribosomal protein L20
        rplU BSU27960 Yes Yes 3J9W B. subtilis Ribosomal protein L21
        rplV BSU01210 No Yes 3J9W B. subtilis Ribosomal protein L22
        rplW BSU01180 No Yes 3J9W B. subtilis Ribosomal protein L23
        rplX BSU01270 Yes Yes 3J9W B. subtilis Ribosomal protein L24
        rpmA BSU27940 Yes Yes 3J9W B. subtilis Ribosomal protein L27
        rpmB BSU15820 No 3J9W B. subtilis Ribosomal protein L28
        rpmC BSU01240 No 3J9W B. subtilis Ribosomal protein L29
        rpmD BSU01340 Yes 3J9W B. subtilis Ribosomal protein L30
        rpmE BSU37070 No 3J9W B. subtilis Ribosomal protein L31
        rpmF BSU15080 No 3J9W B. subtilis Ribosomal protein L32
        rpmGA BSU24900 No 3J9W B. subtilis Ribosomal protein L33a
        rpmGB BSU00990 No 3J9W B. subtilis Ribosomal protein L33b
        rpmH BSU41060 No 3J9W B. subtilis Ribosomal protein L34
        rpmI BSU28860 No 3J9W B. subtilis Ribosomal protein L35
        rpmJ BSU01400 No Yes 3J9W B. subtilis Ribosomal protein L36
        rpsB BSU16490 Yes Yes 3J9W B. subtilis Ribosomal protein S2
        rpsC BSU01220 Yes Yes 3J9W B. subtilis Ribosomal protein S3
        rpsD BSU29660 Yes Yes 3J9W B. subtilis Ribosomal protein S4
        rpsE BSU01330 Yes Yes 3J9W B. subtilis Ribosomal protein S5
        rpsF BSU40910 No Yes 3J9W B. subtilis Ribosomal protein S6
        rpsG BSU01110 Yes Yes 3J9W B. subtilis Ribosomal protein S7
        rpsH BSU01300 Yes Yes 3J9W B. subtilis Ribosomal protein S8
        rpsI BSU01500 Yes Yes 3J9W B. subtilis Ribosomal protein S9
        rpsJ BSU01150 Yes Yes 3J9W B. subtilis Ribosomal protein S10
        rpsK BSU01420 Yes Yes 3J9W B. subtilis Ribosomal protein S11
        rpsL BSU01100 Yes Yes 3J9W B. subtilis Ribosomal protein S12
        rpsM BSU01410 Yes Yes 3J9W B. subtilis Ribosomal protein S13
        rpsN BSU01290 Yes Yes 3J9W B. subtilis Ribosomal protein S14
        rpsO BSU16680 Yes Yes 3J9W B. subtilis Ribosomal protein S15
        rpsP BSU15990 Yes Yes 3J9W B. subtilis Ribosomal protein S16
        rpsQ BSU01250 Yes Yes 3J9W B. subtilis Ribosomal protein S17
        rpsR BSU40890 Yes Yes 3J9W B. subtilis Ribosomal protein S18
        rpsS BSU01200 Yes Yes 3J9W B. subtilis Ribosomal protein S19
        rpsT BSU25550 No 3J9W B. subtilis Ribosomal protein S20
        rpsU BSU25410 No 3J9W B. subtilis Ribosomal protein S21
    rRNA/tRNA maturation and modification
        rnpA BSU41050 Yes Yes 3.1.26.5 3Q1R T. maritima Protein component of RNase P
        rnpB BSU_misc_RNA_35 Yes 3Q1R T. maritima RNA component of RNase P
        rnz BSU23840 Yes 3.1.26.11 4GCW B. subtilis RNase Z
        rph BSU28370 No 2.7.7.56 1OYP B. subtilis RNase PH
        rbfA BSU16650 No 1JOS Haemophilus influenzae Ribosome-binding factor A
        rimM BSU16020 No 3H9N H. influenzae 16S rRNA-processing protein, RNase
        cca BSU22450 Yes 2.7.7.25 1MIY G. stearothermophilus tRNA nucleotidyltransferase
        fmt BSU15730 Yes Yes 2.1.2.9 4IQF Bacillus anthracis Methionyl-tRNA formyltransferase
        folD BSU24310 Yes Yes 1.5.1.5 1B0A E. coli Methylenetetrahydrofolate dehydrogenase
        rlmCD BSU06730 No 2.1.1.190 2BH2 E. coli rRNA methyltransferase
        ysgA BSU28650 Yes Yes 2.1.1.- 4X3M T. thermophilus Similar to rRNA methylase
        mraW BSU15140 No Yes 2.1.1.199 1WG8 T. thermophilus SAM-dependent methyltransferase
        cspR BSU08930 Yes 2.1.1.- 4PZK B. anthracis Similar to tRNA(Um34/Cm34) methyltransferase
        trmD BSU16030 Yes Yes 2.1.1.31 3KY7 S. aureus tRNA methyltransferase
        trmU BSU27500 Yes Yes 2.8.1.- 2HMA S. pneumoniae tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase
        yrvO BSU27510 Yes 2.8.1.7 1P3W E. coli Cysteine desulfurase
        yacO BSU00960 No Yes 2.1.1.- 1GZ0 E. coli Putative 23S rRNA methyltransferase
        ksgA BSU00420 No Yes 2.1.1.- 3FUU T. thermophilus rRNA adenine dimethyltransferase
        rluB BSU23160 No Yes 5.4.99.22 4LAB E. coli Pseudouridine synthase
        ypuI BSU23200 No rRNA pseudouridine 2633 synthase
        tilS BSU00670 Yes Yes 6.3.4.19 3A2K G. kaustophilus tRNAIle lysidine synthetase
        tsaB BSU05920 Yes 2A6A T. maritima Threonyl carbamoyl adenosine (t6A) modification of tRNAs that pair with ANN codons in mRNA
        tsaD BSU05940 Yes Yes 2.3.1.234 3ZET Salmonella enterica serovar Typhimurium Threonyl carbamoyl adenosine (t6A) modification of tRNAs that pair with ANN codons in mRNA, universally conserved protein
        tsaC BSU36950 No 2.7.7.87 3AJE Sulfolobus tokodaii l-Threonyl carbamoyl AMP synthase, biosynthesis of the hypermodified base threonyl carbamoyl adenosine [t(6)A]
        gidA BSU41010 No Yes 3CP2 E. coli tRNA uridine 5-carboxymethyl-aminomethyl modification enzyme
        thdF BSU41020 No Yes 1XZP T. maritima GTP-binding protein, putative tRNA modification GTPase
        truA BSU01480 No Yes 5.4.99.12 1VS3 T. thermophilus Pseudouridylate synthase I, universally conserved protein
        tsaE BSU05910 No Yes 1HTW H. influenzae P-loop ATPase
        trmFO BSU16130 No Yes 2.1.1.74 3G5Q T. thermophilus tRNA:m(5)U-54 methyltransferase
        miaA BSU17330 No 2.5.1.8 2QGN Bacillus halodurans tRNA isopentenylpyrophosphate transferase
        yaaJ BSU00180 No 2B3J S. aureus tRNA-specific adenosine deaminase
        ylyB BSU15460 No Yes 5.4.99.23 1V9F E. coli Similar to pseudouridylate synthase
    Ribosome maturation/assembly
        ydiD BSU05930 No 2.3.1.128 2CNM S. enterica Similar to ribosomal protein alanine N-acetyltransferase
        ylxS BSU16590 No 1IB8 S. pneumoniae Similar to 30S ribosomal subunit maturation protein
        prp BSU27950 No 4PEO S. aureus Maturation of L27
        engA BSU22840 Yes 2HJG B. subtilis GTPase, ribosome 50S subunit assembly
        era BSU25290 Yes Yes 3R9W A. aeolicus GTP-binding protein
        obg BSU27920 Yes Yes 3.6.5.- 1LNZ B. subtilis GTP-binding protein
        rbgA BSU16050 Yes Yes 1PUJ B. subtilis Assembly of the 50S subunit of the ribosome
        yqeH BSU25670 Yes 3H2Y B. anthracis Assembly/stability of the 30S subunit of the ribosome, assembly of the 70S ribosome
        ysxC BSU28190 Yes Yes 1SVI B. subtilis Assembly of the 50S subunit of the ribosome
    Translation factors
        efp BSU24450 No Yes 1YBY Clostridium thermocellum Elongation factor P
        frr BSU16520 Yes Yes 4GFQ B. anthracis Ribosome recycling factor
        fusA BSU01120 Yes Yes 2XEX S. aureus Elongation factor G
        infA BSU01390 Yes Yes 4QL5 S. pneumoniae Translation initiation factor IF-1
        infB BSU16630 Yes Yes 1ZO1 E. coli Translation initiation factor IF-2
        infC BSU28870 Yes Yes 1TIG G. stearothermophilus Translation initiation factor IF-3
        prfA BSU37010 Yes Yes 1ZBT Streptococcus mutans Peptide chain release factor 1
        prfB BSU35290 Yes 1MI6 E. coli Peptide chain release factor 2
        tsf BSU16500 Yes Yes 1EFU E. coli Elongation factor Ts
        tufA BSU01130 Yes Yes 3.6.5.3 4R71 E. coli Elongation factor Tu
        lepA BSU25510 No Yes 4QJT T. thermophilus Elongation factor 4
    Translation/others
        map BSU01380 Yes Yes 3.4.11.18 1O0X T. maritima Methionine aminopeptidase
        ywkE BSU37000 No Yes 2.1.1.297 2B3T E. coli Similar to N5-glutamine methyltransferase that modifies peptide release factors
        ybxF BSU01090 No 3V7E B. subtilis Similar to ribosomal protein L7 family
        spoVC BSU00530 Yes Yes 3.1.1.29 4QT4 S. pyogenes Putative peptidyl-tRNA hydrolase
        ssrA BSU_MISC_RNA_55 No 1P6V A. aeolicus tmRNA
        smpB BSU33600 No Yes 1P6V A. aeolicus tmRNA-binding protein
    Protein secretion
        scr BSU_misc_RNA_2 Yes 4UE5 B. subtilis Signal recognition particle RNA
        ffh BSU15980 Yes Yes 4UE5 B. subtilis Signal recognition particle component
        ftsY BSU15950 No Yes 2XXA E. coli Signal recognition particle
        yidC2 BSU23890 No 3WO6 B. halodurans Sec-independent membrane protein translocase
        secA BSU35300 Yes Yes 3DL8 B. subtilis Preprotein translocase subunit (ATPase)
        secE BSU01000 Yes 3DL8 B. subtilis Preprotein translocase subunit
        secY BSU01360 Yes Yes 3DL8 B. subtilis Preprotein translocase subunit, universally conserved protein
        secG BSU33630 No 3DL8 B. subtilis Preprotein translocase subunit
        sipS BSU23310 No 4NV4 B. anthracis Signal peptidase I
        prsA BSU09950 Yes 5.2.1.8 4WO7 B. subtilis Protein secretion (posttranslocation molecular chaperone)
        csaA BSU19040 No 2NZH B. subtilis Molecular chaperone involved in protein secretion
        lgt BSU34990 No 2.4.99.- 5AZB E. coli Prolipoprotein diacylglyceryl transferase
        lspA BSU15450 No 5DIR P. aeruginosa Signal peptidase II
    Proteolysis/quality control/chaperones
        htrB BSU33000 No 3QO6 Arabidopsis thaliana Serine protease
        groES BSU06020 Yes 1WE3 T. thermophilus Chaperonin, universally conserved protein
        groEL BSU06030 Yes 1WE3 T. thermophilus Chaperonin
        dnaJ BSU25460 No Yes 3LZ8 K. pneumoniae Activation of DnaK
        dnaK BSU25470 No Yes 2V7Y G. kaustophilus Molecular chaperone
        grpE BSU25480 No 4ANI G. kaustophilus Activation of DnaK
        tig BSU28230 No 2MLX E. coli Trigger factor (prolyl isomerase)
Metabolism
    Central carbon metabolism
        Glycolysis
            ptsG BSU13890 No Yes 2.7.1.69 PTS glucose permease, EIICBA(Glc)
            ptsH BSU13900 No Yes 2.7.11.- 2FEP B. subtilis HPr, general component of the PTS
            ptsI BSU13910 No Yes 2.7.3.9 2WQD S. aureus Enzyme I, general component of the PTS
            pgi BSU31350 No Yes 5.3.1.9 3IFS B. anthracis Glucose-6-phosphate isomerase
            pfkA BSU29190 No Yes 2.7.1.11 4A3S B. subtilis Phosphofructokinase
            fbaA BSU37120 No 4.1.2.13 4TO8 S. aureus Fructose 1,6-bisphosphate aldolase
            tpi BSU33920 No Yes 5.3.1.1 2BTM G. stearothermophilus Triose phosphate isomerase
            gapA BSU33940 Yes Yes 1.2.1.12 1GD1 G. stearothermophilus Glyceraldehyde-3-phosphate dehydrogenase
            pgk BSU33930 No Yes 2.7.2.3 1PHP G. stearothermophilus Phosphoglycerate kinase, universally conserved protein
            pgm BSU33910 Yes Yes 5.4.2.1 1EJJ G. stearothermophilus Phosphoglycerate mutase
            eno BSU33900 Yes Yes 4.2.1.11 4A3R B. subtilis Enolase, universally conserved protein
            pyk BSU29180 No Yes 2.7.1.40 2E28 G. stearothermophilus Pyruvate kinase
            pdhA BSU14580 Yes Yes 1.2.4.1 3DUF G. stearothermophilus Pyruvate dehydrogenase (E1 alpha subunit)
            pdhB BSU14590 No Yes 1.2.4.1 3DUF G. stearothermophilus Pyruvate dehydrogenase (E1 beta subunit)
            pdhC BSU14600 No Yes 2.3.1.12 3DUF G. stearothermophilus Pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit)
            pdhD BSU14610 No Yes 1.8.1.4 1EBD G. stearothermophilus Dihydrolipoamide dehydrogenase E3 subunit of both pyruvate and 2-oxoglutarate dehydrogenase complexes
        Transhydrogenation cycle
            ytsJ BSU29220 No 1.1.1.38 2A9F S. pyogenes Malic enzyme
            malS BSU29880 No 1.1.1.38 1LLQ Ascaris suum Malate dehydrogenase (decarboxylating)
        Pentose phosphate pathway
            ykgB BSU13010 No 3.1.1.31 3HFQ Lactobacillus plantarum 6-Phosphogluconolactonase
            rpe BSU15790 No Yes 5.1.3.1 1TQJ Synechocystis sp. Ribulose 5-phosphate 3-epimerase
            tkt BSU17890 No Yes 2.2.1.1 3HYL B. anthracis Transketolase
            zwf BSU23850 No 1.1.1.49 1DPG Leuconostoc mesenteroides Glucose-6-phosphate dehydrogenase
            gndA BSU23860 No 1.1.1.44 2W8Z G. stearothermophilus NADP-dependent phosphogluconate dehydrogenase
            ywlF BSU36920 No Yes 3HE8 C. thermocellum Ribose-5-phosphate isomerase
            ywjH BSU37110 No 2.2.1.2 3R8R B. subtilis Transaldolase
        Recycling of acetate
            acsA BSU29680 No 6.2.1.1 2P2F S. enterica Acetyl-CoA synthetase
    Respiration/energy
            ndh BSU12290 No 4NWZ Caldalkalibacillus thermarum NADH dehydrogenase
        Cytochrome aa3
            qoxD BSU38140 No Cytochrome aa3 quinol oxidase (subunit IV)
            qoxC BSU38150 No 1FFT E. coli Cytochrome aa3 quinol oxidase (subunit III)
            qoxB BSU38160 No 1FFT E. coli Cytochrome aa3 quinol oxidase (subunit I)
            qoxA BSU38170 No 1FFT E. coli Cytochrome aa3 quinol oxidase (subunit II)
        Cytochrome maturation
            resC BSU23130 Yes Part of heme translocase, required for cytochrome c synthesis
            resB BSU23140 Yes Part of heme translocase, required for cytochrome c synthesis
        ATPase
            atpC BSU36800 No 2E5Y Bacillus sp. ATP synthase, F1 (subunit epsilon)
            atpD BSU36810 No Yes 3.6.3.14 1SKY Bacillus sp. ATP synthase, F1 (subunit beta)
            atpG BSU36820 No Yes 4XD7 G. kaustophilus ATP synthase, F1 (subunit gamma)
            atpA BSU36830 No Yes 3.6.3.14 1SKY Bacillus sp. ATP synthase, F1 (subunit alpha)
            atpH BSU36840 No ATP synthase, F1 (subunit delta)
            atpF BSU36850 No Yes ATP synthase, Fo (subunit b)
            atpE BSU36860 No 1WU0 Bacillus sp. ATP synthase, Fo (subunit c)
            atpB BSU36870 No 1C17 E. coli ATP synthase, Fo (subunit a)
            atpI BSU36880 No ATP synthase (subunit i)
    Amino acids
        Asp, Glu
            gltT BSU10220 No 3V8F P. horikoshii Major H+/Na+-glutamate symport protein
        Arg
            rocE BSU40330 No 3LRB E. coli Amino acid permease
        Pro
            putP BSU03220 No 2XQ2 Vibrio parahaemolyticus High-affinity proline permease
        Trp
            trpP BSU10010 No S protein of tryptophan ECF transporter
        Met
            metQ BSU32730 No 4GOT B. subtilis Methionine ABC transporter (binding lipoprotein)
            metP BSU32740 No 3DHW E. coli Methionine ABC transporter, permease
            metN BSU32750 No 3DHW E. coli Methionine ABC transporter (ATP-binding protein)
        His
            hutM BSU39390 No Histidine permease
        Cys
            tcyP BSU09130 No Yes 3KBC P. horikoshii Cystine transporter
        Gly
            glyA BSU36900 Yes Yes 2.1.2.1 1KKJ G. stearothermophilus Serine hydroxymethyltransferase
        Ile, Val, Thr
            bcaP BSU09460 No Branched-chain amino acid transporter
        Lys
            yvsH BSU33330 No 3LRB E. coli Putative lysine transporter
        Chorismate for aromatic amino acids, menaquinone, and folate
            aroA BSU29750 No 2.5.1.54 3NVT L. monocytogenes 3-Deoxy-d-arabino-heptulosonate 7-phosphate synthase/chorismate mutase isozyme 3
            aroB BSU22700 No 4.2.3.4 3CLH Helicobacter pylori 3-Dehydroquinate synthase
            aroC BSU23080 No 4.2.1.10 1QFE S. enterica serovar Typhi 3-Dehydroquinate dehydratase
            aroD BSU25660 No 1.1.1.25 2EGG G. kaustophilus Shikimate dehydrogenase
            aroE BSU22600 No 2.5.1.19 3RMT B. halodurans 3-Phosphoshikimate 1-carboxyvinyltransferase
            aroF BSU22710 No 4.2.3.5 1Q1L A. aeolicus Chorismate synthase
            aroK BSU03150 No 2.7.1.71 2PT5 A. aeolicus Shikimate kinase
        Phe, Tyr
            pheA BSU27900 No 4.2.1.51 4LUB S. mutans Prephenate dehydratase
            hisC BSU22620 No 2.6.1.9 3FFH Listeria innocua Histidinol-phosphate aminotransferase/tyrosine and phenylalanine aminotransferase
            aroH BSU22690 No 1COM B. subtilis Chorismate mutase (isozymes 1 and 2)
            tyrA BSU22610 No 1.3.1.12 3DZB Streptococcus thermophilus Prephenate dehydrogenase
        Asn
            asnB BSU30540 No 6.3.5.4 1CT9 E. coli Asparagine synthase (glutamine hydrolyzing)
        Ala, Ser
            alaT BSU31400 No 2.6.1.- 1DJU P. horikoshii Alanine aminotransferase
            serA BSU23070 No 1.1.1.95 1YGY Mycobacterium tuberculosis Phosphoglycerate dehydrogenase
            serC BSU10020 No 2.6.1.52 1W23 Bacillus alcalophilus 3-Phosphoserine aminotransferase
            ywtE BSU35850 No 1NRW B. subtilis Putative phosphatase
        Leu
            yvbW BSU34010 No 3GI9 Methanocaldococcus jannaschii Putative leucine permease
        Gln
            glnA BSU17460 No 6.3.1.2 4S0R B. subtilis Glutamine synthetase
    Nucleotides/phosphate
        PRPP
            prs BSU00510 Yes Yes 2.7.6.1 1DKR B. subtilis Phosphoribosylpyrophosphate synthetase, universally conserved protein
        Pyrimidine biosynthesis
            pyrAA BSU15510 No 6.3.5.5 1JDB E. coli Carbamoyl-phosphate synthetase (glutaminase subunit)
            pyrAB BSU15520 No 6.3.5.5 1JDB E. coli Carbamoyl-phosphate synthetase (catalytic subunit)
            pyrB BSU15490 No 2.1.3.2 3R7D B. subtilis Aspartate carbamoyltransferase
            pyrC BSU15500 No 3.5.2.3 3MPG B. anthracis Dihydro-orotase
            pyrD BSU15540 No 1.3.3.1 1EP1 Lactococcus lactis Dihydro-orotic acid dehydrogenase (catalytic subunit)
            pyrE BSU15560 No 2.4.2.10 3M3H B. anthracis Orotate phosphoribosyltransferase
            pyrF BSU15550 No 4.1.1.23 1DBT B. subtilis Orotidine 5′-phosphate decarboxylase
            cmk BSU22890 Yes Yes 2.7.4.14 1Q3T S. pneumoniae Cytidylate kinase (CMP, dCMP)
            pyrG BSU37150 Yes Yes 6.3.4.2 1S1M E. coli CTP synthase (NH3, glutamine)
            yncF BSU17660 No 2XCD B. subtilis dUTPase
            thyB BSU21820 No 2.1.1.45 3IX6 Brucella melitensis Thymidylate synthase B
            tmk BSU00280 Yes Yes 2.7.4.9 2CCJ S. aureus Thymidylate kinase
        Purine biosynthesis
            purF BSU06490 No 2.4.2.14 1GPH B. subtilis Glutamine phosphoribosyldiphosphate amidotransferase
            purD BSU06530 No 6.3.4.13 2XD4 B. subtilis Phosphoribosylglycinamide synthetase
            purN BSU06510 No 2.1.2.2 3AV3 G. kaustophilus Phosphoribosylglycinamide formyltransferase
            purS BSU06460 No 1TWJ B. subtilis Phosphoribosylformylglycinamidine synthase
            purQ BSU06470 No 6.3.5.3 3D54 T. maritima Phosphoribosylformylglycinamidine synthase
            purL BSU06480 No 6.3.5.3 3VIU T. thermophilus Phosphoribosylformylglycinamidine synthase
            purM BSU06500 No 6.3.3.1 2BTU B. anthracis Phosphoribosylaminoimidazole synthetase
            purE BSU06420 No 4.1.1.21 1XMP B. anthracis Phosphoribosylaminoimidazole carboxylase (ATP dependent)
            purK BSU06430 No 4.1.1.21 4DLK B. anthracis Phosphoribosylaminoimidazole carboxylase (ATP dependent)
            purC BSU06450 No 6.3.2.6 2YWV G. kaustophilus Phosphoribosylaminoimidazole succinocarboxamide synthase
            purB BSU06440 No 4.3.2.2 1F1O B. subtilis Adenylsuccinate lyase
            purH BSU06520 No 2.1.2.3 3ZZM M. tuberculosis Phosphoribosylaminoimidazole carboxamide formyltransferase
            guaB BSU00090 Yes 1.1.1.205 3TSB B. anthracis IMP dehydrogenase
            guaA BSU06360 No 6.3.5.2 1GPM E. coli GMP synthase (glutamine hydrolyzing)
            gmk BSU15680 Yes Yes 2.7.4.8 3TAU L. monocytogenes Guanylate kinase (GMP:dATP, dGMP:ATP)
            purA BSU40420 No 6.3.4.4 4M0G B. anthracis Adenylosuccinate synthetase
            adk BSU01370 Yes Yes 2.7.4.3 1P3J B. subtilis Adenylate kinase
        Pyrimidine/purine biosynthesis
            nrdE BSU17380 Yes Yes 1PEM S. enterica Ribonucleoside diphosphate reductase (major subunit)
            nrdF BSU17390 Yes Yes 4DR0 B. subtilis Ribonucleoside diphosphate reductase (major subunit)
            nrdI BSU17370 Yes 1RLJ B. subtilis Ribonucleoside diphosphate reductase
            ndk BSU22730 No 2.7.4.6 2VU5 B. anthracis Nucleoside diphosphate kinase
            hprT BSU00680 Yes Yes 2.4.2.8 3H83 B. anthracis Hypoxanthine phosphoribosyltransferase
        Phosphate
            pit BSU12840 No Low-affinity inorganic phosphate transporter
    Lipids
        Malonyl-CoA synthesis
            accC BSU24340 Yes 6.3.4.14 2VPQ S. aureus Acetyl-CoA carboxylase (biotin carboxylase subunit)
            accB BSU24350 Yes 6.4.1.2 4HR7 E. coli Acetyl-CoA carboxylase (biotin carboxyl carrier subunit)
            accA BSU29200 Yes 6.4.1.2 2F9I S. aureus Acetyl-CoA carboxylase (alpha subunit)
            accD BSU29210 Yes 6.4.1.2 2F9I S. aureus Acetyl-CoA carboxylase (beta subunit)
            birA BSU22440 Yes 6.3.4.15 3RIR S. aureus Biotin protein ligase
        Acyl carrier
            acpS BSU04620 Yes 2.7.8.7 1F80 B. subtilis Acyl carrier protein synthase, 4′-phosphopantetheine transferase
            acpA BSU15920 Yes 1F80 B. subtilis Acyl carrier protein
        Aceto-acyl-Acp synthesis
            fabD BSU15900 Yes 2.3.1.39 3QAT Bartonella henselae Malonyl-CoA—acyl carrier protein transacylase
            fabHA BSU11330 No 2.3.1.180 1ZOW S. aureus Beta-ketoacyl–acyl carrier protein synthase III
        β-Ketoacyl-Acp chain elongation
            fabG BSU15910 Yes 1.1.1.100 2UVD B. anthracis Beta-ketoacyl–acyl carrier protein reductase
            fabF BSU11340 Yes 2.3.1.179 4LS5 B. subtilis Beta-ketoacyl–acyl carrier protein synthase II
            fabI BSU11720 No 1.3.1.9 3OIF B. subtilis Enoyl-acyl carrier protein reductase
            ywpB BSU36370 Yes 1U1Z P. aeruginosa β-Hydroxyacyl (acyl carrier protein) dehydratase
        Phosphatidic acid synthesis
            plsC BSU09540 Yes 2.3.1.51 Acyl-ACP:1-acylglycerolphosphate acyltransferase
            plsX BSU15890 Yes Yes 1VI1 B. subtilis Acyl-ACP:phosphate acyltransferase
            plsY BSU18070 Yes Yes Acylphosphate:glycerol-phosphate acyltransferase
            gpsA BSU22830 Yes 1.1.1.94 1Z82 T. maritima Glycerol-3-phosphate dehydrogenase (NAD)
        Phosphatidylglycerol phosphate synthesis
            cdsA BSU16540 Yes Yes 2.7.7.41 4Q2G T. maritima Phosphatidate cytidylyltransferase
            pgsA BSU16920 Yes Yes 2.7.8.5 Phosphatidylglycerophosphate synthase
    Cofactors
        ECF transporter (general component) for riboflavin, biotin, thiamine, tryptophan
            ybxA BSU01450 No Yes 4HUQ Lactobacillus brevis ATP-binding A1 component of ECF transporters
            ybaE BSU01460 No Yes 4HUQ L. brevis ATP-binding A2 component of ECF transporters
            ybaF BSU01470 No Yes 4HUQ L. brevis Transmembrane T component of ECF transporters
        NAD
            nadD BSU25640 Yes 2.7.7.18 1KAM B. subtilis Nicotinamide-nucleotide adenylyltransferase
            nadE BSU03130 Yes Yes 6.3.1.5 1NSY B. subtilis NH3-dependent NAD+ synthetase
            nadF BSU11610 Yes Yes 2.7.1.23 2I1W L. monocytogenes NAD kinase
            niaP BSU02950 No 4J05 Piriformospora indica Nicotinate transporter
            pncB BSU31750 Yes 2.4.2.11 2F7F E. faecalis Putative nicotinate phosphoribosyltransferase
        Riboflavin/FAD
            ribC BSU16670 Yes 2.7.1.26 3OP1 S. pneumoniae Riboflavin kinase/FAD synthase
            ribU BSU23050 No 3P5N S. aureus Riboflavin ECF transporter, S protein
        Pyridoxal phosphate
            pdxS BSU00110 No 2NV2 B. subtilis Pyridoxal-5′-phosphate synthase (synthase domain)
            pdxT BSU00120 No 2NV2 B. subtilis Pyridoxal-5′-phosphate synthase (glutaminase domain)
        Biotin
            yhfU BSU10370 No 4DVE L. lactis S protein of biotin ECF transporter
        Thiamine, TPP
            yloS BSU15800 No 2.7.6.2 3LM8 B. subtilis Thiamine pyrophosphokinase
            thiT BSU30990 No 4MES L. lactis S protein of thiamine ECF transporter
        Lipoate
            gcvH BSU32800 No 3IFT M. tuberculosis Glycine cleavage system protein H, 2-oxo acid dehydrogenase
            lipM BSU24530 No 3A7A E. coli Octanoyltransferase
            lipL BSU37640 No 2P5I B. halodurans GcvH:E2 amidotransferase
            lipA BSU32330 Yes 2.8.1.8 4U0O T. elongatus Lipoic acid synthase
        CoA
            ykpB BSU14440 No 3HN2 Geobacter metallireducens Putative ketopantoate reductase
            panD BSU22410 No 4.1.1.11 2C45 M. tuberculosis Aspartate 1-decarboxylase
            panC BSU22420 No 6.3.2.1 2X3F S. aureus Pantothenate synthase
            panB BSU22430 No 2.1.2.11 1M3U E. coli 3-Methyl-2-oxobutanoate hydroxymethyltransferase
            ybgE BSU02390 No 2.6.1.42 3HT5 M. tuberculosis Branched-chain amino acid aminotransferase
            coaA BSU23760 No 2.7.1.33 4F7W K. pneumoniae Probable pantothenate kinase
            yloI BSU15700 No 4.1.1.36 1U7U E. coli Coenzyme A biosynthesis bifunctional protein CoaBC
            ylbI BSU15020 No 2.7.7.3 1O6B B. subtilis Pantetheine-phosphate adenylyltransferase
            ytaG BSU29060 Yes 2.7.1.24 4TTP Legionella pneumophila Dephospho-CoA kinase
        SAM
            metK BSU30550 Yes Yes 2.5.1.6 1FUG E. coli S-Adenosylmethionine synthetase
        Folate
            folE BSU22780 No 3.5.4.16 4UQF L. monocytogenes GTP cyclohydrolase I
            phoB BSU05740 No 3.1.3.1 3A52 Shewanella sp. Alkaline phosphatase A
            folB BSU00780 No 4.1.2.25 1RRI S. aureus Dihydroneopterin aldolase
            folK BSU00790 No 2.7.6.3 4CYU S. aureus 2-Amino-4-hydroxy-6-hydroxymethyl-dihydropteridine diphosphokinase
            sul BSU00770 No 2.5.1.15 1TWS B. anthracis Dihydropteroate synthase
            folC BSU28080 No Yes 6.3.2.17 1O5Z T. maritima Folyl-polyglutamate synthetase
            dfrA BSU21810 Yes 1.5.1.3 1ZDR G. stearothermophilus Dihydrofolate reductase
            pabB BSU00740 No 2.6.1.85 5CWA M. tuberculosis p-Aminobenzoate synthase (subunit A)
            pabA BSU00750 No 2.6.1.85 1I1Q S. enterica serovar Typhimurium p-Aminobenzoate synthase (subunit B)/anthranilate synthase (subunit II)
            pabC BSU00760 No 4.1.3.38 4WHX Burkholderia pseudomallei Aminodeoxychorismate lyase
            gsaB BSU08710 No 5.4.3.8 3L44 B. anthracis Formate dehydrogenase
            ykkE BSU13110 No 3.5.1.10 3W7B T. thermophilus Formyltetrahydrofolate deformylase
            yoaE BSU18570 No Formate dehydrogenase
        Heme biosynthesis
            hemE BSU10120 No 4.1.1.37 2INF B. subtilis Glutamate-1-semialdehyde aminotransferase
            hemH BSU10130 No 1C1H B. subtilis Uroporphyrinogen decarboxylase (uroporphyrinogen III)
            hemY BSU10140 No 1.3.3.4 3I6D B. subtilis Ferrochelatase
            ctaA BSU14870 No Protoporphyrinogen IX oxidase
            ctaB BSU14880 No Heme A synthase
            hemL BSU28120 No 5.4.3.8 3BS8 B. subtilis Heme O synthase (major enzyme)
            hemB BSU28130 No 4.2.1.24 1W5Q P. aeruginosa Glutamate-1-semialdehyde aminotransferase
            hemD BSU28140 No 4.2.1.75 Porphobilinogen synthase
            hemC BSU28150 No 2.5.1.61 4MLQ Bacillus megaterium Uroporphyrinogen III synthase
            hemX BSU28160 No Hydroxymethylbilane synthase
            hemA BSU28170 No 1.2.1.70 4N7R A. thaliana Glutamyl-tRNA reductase
            hemQ BSU37670 No 1T0T G. stearothermophilus Heme-binding protein
        Menaquinone
            menA BSU38490 Yes Probable 1,4-dihydroxy-2-naphthoate octaprenyltransferase
            menH BSU22750 No 4OBW Saccharomyces cerevisiae Menaquinone biosynthesis methyltransferase
            menC BSU30780 Yes 4.2.1.113 1WUE E. faecalis O-Succinylbenzoate-CoA synthase
            menE BSU30790 Yes 6.2.1.26 5BUQ B. subtilis O-Succinylbenzoate-CoA ligase
            menB BSU30800 Yes 4.1.3.36 2IEX G. kaustophilus Naphthoate synthase
            menD BSU30820 Yes 2.2.1.9 2X7J B. subtilis 2-Succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase/2-oxoglutarate decarboxylase
            ytxM BSU30810 No 2XMZ S. aureus Similar to prolyl aminopeptidase
            menF BSU30830 No 5.4.4.2 3HWO E. coli Menaquinone-specific isochorismate synthase
    Metals and iron-sulfur clusters
        Sodium export
            mrpA BSU31600 Yes 4HE8 T. thermophilus Na+/H+ antiporter subunit
            mrpB BSU31610 Yes Na+/H+ antiporter subunit
            mrpC BSU31620 Yes Na+/H+ antiporter subunit
            mrpD BSU31630 Yes 4HE8 T. thermophilus Na+/H+ antiporter subunit
            mrpE BSU31640 No Na+/H+ antiporter subunit
            mrpF BSU31650 Yes Na+/H+ antiporter subunit
            mrpG BSU31660 No Na+/H+ antiporter subunit
        Potassium
            ktrD BSU13500 No Yes 4J7C B. subtilis Potassium transporter KtrCD
            ktrC BSU14510 No Yes 4J90 B. subtilis Potassium transporter KtrCD
        Iron
            efeO BSU38270 No 3AT7 Sphingomonas sp. Lipoprotein, elemental iron uptake system (binding protein)
            efeU BSU38280 No Elemental iron uptake system (permease)
            yfmF BSU07490 No 4G1U Yersinia pestis Iron/citrate ABC transporter (ATP-binding protein)
            yfmE BSU07500 No 4G1U Y. pestis Iron/citrate ABC transporter (permease)
            yfmD BSU07510 No 4G1U Y. pestis Iron/citrate ABC transporter (permease)
            yfmC BSU07520 No 3EIW S. aureus Iron/citrate ABC transporter (binding protein)
            yhfQ BSU10330 No 3EIW S. aureus Iron/citrate ABC transporter (solute-binding protein)
        Magnesium
            mgtE BSU13300 No 2YVX T. thermophilus Primary magnesium transporter
            mntH BSU04360 No 4WGV Staphylococcus capitis Manganese transporter (proton symport)
        Zinc
            znuA BSU02850 No 2O1E B. subtilis ABC transporter for zinc (binding protein)
            znuC BSU02860 No 4YMS Caldanaerobacter subterraneus ABC transporter for zinc (ATP-binding protein)
            znuB BSU02870 No ABC transporter for zinc (permease)
        Copper
            ycnJ BSU03950 No Copper transporter
        Fe-S cluster
            sufB BSU32670 Yes 5AWF E. coli Synthesis of Fe-S clusters
            sufU BSU32680 Yes Yes 1XJS B. subtilis Iron-sulfur cluster scaffold protein
            sufD BSU32700 Yes 5AWF E. coli Synthesis of Fe-S clusters
            sufS BSU32690 Yes Yes 2.8.1.7 1T3I Synechocystis sp. Cysteine desulfurase
            sufC BSU32710 Yes 2D2E T. thermophilus ABC transporter (ATP-binding protein)
            fra BSU05750 No 2OC6 B. subtilis Frataxin-like protein
            yutI BSU32220 No 1XHJ Staphylococcus epidermidis Putative iron-sulfur scaffold protein
    Cell division
    Cell wall synthesis
        Synthesis of d-glutamate
            racE BSU28390 Yes 5.1.1.3 1ZUW B. subtilis Glutamate racemase
        Synthesis of d-Ala-d-Ala
            alr BSU04640 Yes 5.1.1.1 3ZM5 S. pneumoniae Alanine racemase
            ddl BSU04560 Yes 6.3.2.4 2I80 S. aureus d-Alanine-d-alanine ligase
        Synthesis of m-diaminopimelate
            dapG BSU16760 No 2.7.2.4 1SFT G. stearothermophilus Aspartokinase I (alpha and beta subunits)
            asd BSU16750 Yes 1.2.1.11 2GYY S. pneumoniae Aspartate-semialdehyde dehydrogenase
            dapA BSU16770 Yes 4.2.1.52 1XKY B. anthracis Dihydrodipicolinate synthase
            dapB BSU22490 Yes 1.3.1.26 5EER Corynebacterium glutamicum Dihydrodipicolinate reductase (NADPH)
            ykuQ BSU14180 Yes 2.3.1.89 3R8Y B. anthracis Similar to tetrahydrodipicolinate succinylase
            patA BSU14000 Yes 1GDE P. horikoshii Aminotransferase
            dapI BSU14190 Yes 3.5.1.47 1YSJ B. subtilis N-Acetyl-diaminopimelate deacetylase
            dapF BSU32170 Yes 5.1.1.7 2OTN B. anthracis Diaminopimelate epimerase
        Isoprenoid biosynthesis
            dxs BSU24270 Yes 2.2.1.7 2O1S E. coli 1-Deoxyxylulose-5-phosphate synthase
            ispC BSU16550 Yes 1.1.1.267 1R0K Zymomonas mobilis 1-Deoxy-d-xylulose-5-phosphate reductoisomerase
            ispD BSU00900 Yes 2.7.7.60 2YC3 A. thaliana 2-C-Methyl-d-erythritol 4-phosphate cytidylyltransferase
            ispE BSU00460 Yes 2.7.1.148 3PYD M. tuberculosis 4-Diphosphocytidyl-2-C-methyl-d-erythritol kinase
            ispF BSU00910 Yes 4.6.1.12 3GHZ S. enterica serovar Typhimurium 2-C-Methyl-d-erythritol-2,4-cyclodiphosphate synthase
            ispG BSU25070 Yes 3NOY A. aeolicus Similar to peptidoglycan acetylation, 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate synthase
            ispH BSU25160 Yes 4N7B Plasmodium falciparum (E)-4-Hydroxy-3-methylbut-2-enyl diphosphate reductase
            fni BSU22870 No 5.3.3.2 1P0K B. subtilis Isopentenyl diphosphate isomerase
        Undecaprenyl phosphate biosynthesis
            yqiD BSU24280 No 2.5.1.10 1RTR S. aureus Geranyltransferase
            uppS BSU16530 Yes 2.5.1.31 1F75 Micrococcus luteus Probable undecaprenyl pyrophosphate synthetase
            bcrC BSU36530 No Undecaprenyl pyrophosphate phosphatase
            hepT BSU22740 Yes 2.5.1.30 3AQB M. luteus Heptaprenyl diphosphate synthase component II
            hepS BSU22760 Yes 2.5.1.30 Heptaprenyl diphosphate synthase component I
        Peptidoglycan biosynthesis
            glmS BSU01780 Yes 2.6.1.16 4AMV E. coli Glutamine:fructose-6-phosphate transaminase
            glmM BSU01770 Yes 5.4.2.10 3PDK B. anthracis Phosphoglucosamine mutase
            gcaD BSU00500 Yes 2.7.7.23 4AAW S. pneumoniae UDP-N-acetylglucosamine pyrophosphorylase
            murAA BSU36760 Yes 2.5.1.7 3SG1 B. anthracis UDP-N-acetylglucosamine 1-carboxyvinyltransferase
            murB BSU15230 Yes 1.1.1.158 4PYT Unidentified UDP-N-acetylenolpyruvoylglucosamine reductase
            murC BSU29790 Yes 6.3.2.8 1GQQ H. influenzae UDP-N-acetylmuramoyl-l-alanine synthetase
            murD BSU15200 Yes 6.3.2.9 3LK7 Streptococcus agalactiae UDP-N-acetylmuramoyl-l-alanyl-d-glutamate synthetase
            murE BSU15180 Yes 6.3.2.13 4C13 S. aureus UDP-N-acetylmuramoyl-l-alanyl-d-glutamyl-meso-2,6-diaminopimelate synthetase
            murF BSU04570 Yes 6.3.2.10 1GG4 E. coli UDP-N-acetylmuramoyl-l-alanyl-d-glutamyl-meso-2,6-diaminopimeloyl-d-alanyl-d-alanine synthetase
            mraY BSU15190 Yes 2.7.8.13 4J72 A. aeolicus Phospho-N-acetylmuramoyl-pentapeptide transferase (meso-2,6-diaminopimelate)
            murG BSU15220 Yes 2.4.1.227 1F0K E. coli UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
            murJ BSU30050 No Lipid II flippase
        Peptidoglycan polymerization
            ponA BSU22320 No 3DWK S. aureus Penicillin-binding protein 1A/1B
        PG cross-links, cell separation
            pbpB BSU15160 Yes 1RP5 S. pneumoniae Penicillin-binding protein 2B
            pbpA BSU25000 No 3VSK S. aureus Penicillin-binding protein 2A
            lytE BSU09420 No 4XCM T. thermophilus Cell wall hydrolase (major autolysin) for cell elongation and separation
            lytF BSU09370 No 4XCM T. thermophilus Gamma-d-glutamate-meso-diaminopimelate muropeptidase (major autolysin)
        Wall teichoic acid
            tagO BSU35530 Yes 4J72 A. aeolicus Undecaprenyl phosphate-GlcNAc-1-phosphate transferase
            mnaA BSU35660 Yes 5.1.3.14 4FKZ B. subtilis UDP-N-acetylglucosamine 2-epimerase
            tagA BSU35750 Yes 2.4.1.187 UDP-N-acetyl-d-mannosamine transferase
            tagB BSU35760 Yes 3L7I S. epidermidis Putative CDP-glycerol:glycerol phosphate glycerophosphotransferase
            tagD BSU35740 Yes 2.7.7.39 1COZ B. subtilis Glycerol-3-phosphate cytidylyltransferase
            tagF BSU35720 Yes 2.7.8.12 3L7I S. epidermidis CDP-glycerol:polyglycerol phosphate glycerophosphotransferase
            tagH BSU35700 Yes 3.6.3.40 ABC transporter for teichoic acid translocation (ATP-binding protein)
            tagG BSU35710 Yes ABC transporter for teichoic acid translocation (permease)
            tagU BSU35650 No 3OWQ L. innocua Phosphotransferase, attachment of anionic polymers to peptidoglycan
        Lipoteichoic acid
            dgkB BSU06720 Yes 2QV7 S. aureus Diacylglycerol kinase
            pgcA BSU09310 No Yes 5.4.2.2 2Z0F T. thermophilus Alpha-phosphoglucomutase
            gtaB BSU35670 No Yes 2.7.7.9 2UX8 Sphingomonas elodea UTP-glucose-1-phosphate uridylyltransferase
            ltaS BSU07710 No 2W8D B. subtilis Lipoteichoic acid synthase
            ugtP BSU21920 No UDP-glucose diacylglycerol glucosyltransferase
    Coordination
        Divisome
            divIC BSU00620 Yes Cell division initiation protein (septum formation)
            ftsL BSU15150 Yes Cell division protein (septum formation)
            divIB BSU15240 Yes 1YR1 G. stearothermophilus Cell division initiation protein (septum formation)
            ftsZ BSU15290 Yes 2VAM B. subtilis Cell division initiation protein (septum formation)
            ftsW BSU14850 Yes Cell division protein
            ezrA BSU29610 No 4UXV B. subtilis Negative regulator of FtsZ ring formation
            sepF BSU15390 No 3ZIH B. subtilis Part of the divisome
            gpsB BSU22180 No 4UG3 B. subtilis Removal of PBP1 from the cell pole after completion of cell pole maturation
            yvcK BSU34760 No 2HZB B. halodurans Correct localization of PBP1, essential for growth under gluconeogenic conditions
            yvcL BSU34750 No Yes 3HYI T. maritima Involved in Z-ring assembly
        Division site selection
            divIVA BSU15420 No 2WUJ B. subtilis Cell division initiation protein (septum placement)
            minC BSU28000 No 2M4I B. subtilis Cell division inhibitor (septum placement)
            minD BSU27990 No 4V03 A. aeolicus Cell division inhibitor (septum placement)
            noc BSU40990 No 1VZ0 T. thermophilus DNA-binding protein, spatial regulator of cell division to protect the nucleoid, coordination of chromosome segregation and cell division
            minJ BSU35220 No Topological determinant of cell division
        Elongasome
            mreD BSU28010 Yes Cell shape-determining protein, associated with the MreB cytoskeleton
            mreC BSU28020 Yes 2J5U L. monocytogenes Cell shape-determining protein, associated with the MreB cytoskeleton
            mreB BSU28030 Yes 4CZE Caulobacter vibrioides Cell shape-determining protein
            rodA BSU38120 Yes Control of cell shape and elongation
            mreBH BSU14470 No 1JCF T. maritima Cell shape-determining protein
            rodZ BSU16910 Maybe Required for cell shape determination
        Coordination of cell division and DNA replication
            walJ BSU40370 No 4P62 P. aeruginosa Coordination of cell division and DNA replication
    Signaling
        walK BSU40400 Yes 4I5S S. mutans Two-component sensor kinase
        walR BSU40410 Yes 2ZWM B. subtilis Two-component response regulator
        cdaA BSU01750 No 2.7.7.85 4RV7 L. monocytogenes Diadenylate cyclase
        gdpP BSU40510 No c-di-AMP-specific phosphodiesterase
Integrity of the cell
    Protection
        ytbE BSU29050 Yes 3B3D B. subtilis Putative aldo/keto reductase
        katA BSU08820 No 1SI8 E. faecalis Vegetative catalase 1
        sodA BSU25020 No 2RCV B. subtilis Superoxide dismutase
        ahpC BSU40090 No 1WE0 Amphibacillus xylanus Alkyl hydroperoxide reductase (small subunit)
        ahpF BSU40100 No 4O5Q E. coli Alkyl hydroperoxide reductase (large subunit)/NADH dehydrogenase
        trxA BSU28500 Yes Yes 2GZY B. subtilis Antioxidative action by facilitating the reduction of other proteins by cysteine thiol-disulfide exchange
        yumC BSU32110 Yes 1.18.1.2 3LZW B. subtilis Ferredoxin-NAD(P)+ oxidoreductase
        trxB BSU34790 Yes Yes 1.8.1.9 4GCM S. aureus Thioredoxin reductase (NADPH)
    Repair/genome integrity
        hlpB BSU10660 Yes HNH nuclease-like protein, rescues AddA recombination intermediates
        mutY BSU08630 No 5DPK G. stearothermophilus A/G-specific adenine glycosylase
        polY1 BSU23870 No 2.7.7.7 4IRC E. coli Translesion synthesis DNA polymerase Y1
        mutM BSU29080 No 3.2.2.23 1L1T G. stearothermophilus Formamidopyrimidine-DNA glycosidase
        mfd BSU00550 No 2EYQ E. coli Transcription repair-coupling factor
        recD2 BSU27480 No 3E1S Deinococcus radiodurans 5′–3′ DNA helicase replication fork progression
        rnhB BSU16060 No 3O3G T. maritima RNase HII, endoribonuclease
        recA BSU16940 No 1UBC Mycobacterium smegmatis Homologous recombination and DNA repair
Other/unknown
    ppaC BSU40550 Yes 3.6.1.1 1WPM B. subtilis Inorganic pyrophosphatase
    ylaN BSU14840 Yes 2ODM S. aureus Unknown
    yitI BSU11000 No 2JDC Bacillus licheniformis Unknown
    yitW BSU11160 No 3LNO B. anthracis Unknown
    yqhY BSU24330 No Unknown
    ykwC BSU13960 No 3WS7 Pyrobaculum calidifontis Putative beta-hydroxy acid dehydrogenase
    ylbN BSU15070 No Unknown
    ypfD BSU22880 No 4Q7J E. coli Similar to ribosomal protein S1
    yugI BSU31390 No 2K4K B. subtilis Similar to polyribonucleotide nucleotidyltransferase
    floT BSU31010 No Similar to flotillin 1, orchestration of physiological processes in lipid microdomains
    yyaF BSU40920 No Yes 1JAL H. influenzae GTP-binding protein/GTPase
a

The BSU number is the locus tag in the context of the B. subtilis 168 genome (GenBank accession no. NC_000964).

b

The essentiality of a gene refers to wild-type B. subtilis 168. By definition, genes that cannot be deleted as individual genes under defined optimal growth conditions (Luria-Bertani broth with glucose at 37°C) are regarded as being essential.

c

Each gene of the MiniBacillus gene set was tested for the presence of a homolog in Mycoplasma mycoides JCVI-syn3.0 by using a BLASTP analysis.

d

The organism refers to the PDB accession number.

e

PRPP, phosphoribosyl pyrophosphate; TPP, thiamine PPi; SAM, S-adenosylmethionine; PTS, phosphotransferase system; PBP1, penicillin-binding protein 1.